C11H16N2O6 | MD Topology | NMR | X-Ray

Visualize with JSmol

Molecule Information

Molecule Typeheteromolecule
Residue Name (RNME)LXGJ
FormulaC11H16N2O6
IUPAC InChI Key
MKAQFZOQMCAVDN-VAOFZXAKSA-N
IUPAC InChI
InChI=1S/C11H16N2O6/c1-6-4-13(10(17)12-9(6)16)8-3-7(15)11(5-14,18-2)19-8/h4,7-8,14-15H,3,5H2,1-2H3,(H,12,16,17)/t7-,8+,11+/m0/s1
IUPAC Name
1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-5-methoxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione
Common Name
Canonical SMILES (Daylight)
Cc1cn([C@H]2C[C@@H]([C@](O2)(CO)OC)O)c(=O)[nH]c1=O
Number of atoms35
Net Charge0
Forcefieldmultiple
Molecule ID342157
ChEMBL ID 3143909
Visibility Public
Molecule Tags

Format

Molecular Dynamics (MD) Files

Generating ...

X-Ray - Docking Files

Generating ...

NMR Parameters

1H NMR Spectrum

Generating ...

Fragment-Based Charges

No charge assignments available. Use the button above to use OFraMP fragment-based charge assignment.

Topology History

Processing Information

QM Processing Stage

Click table to toggle details.

Processing Stage Template Semi-Empirical QM (QM0) DFT QM (QM1) DFT Hessian QM (QM2)
Calculation None Energy Minization Energy Minization Hessian
Level of Theory None Semi-Empirical / SCF DFT (B3LYP/6-31G*) DFT (B3LYP/6-31G*)
Default Size Limit (Atoms) 2000 500 50 40
Content of MD Topology
Charges Derived From None MOPAC Merz-Singh-Kollman Merz-Singh-Kollman
Geometry  User Provided Optimized Optimized Optimized
Non-Bonded Interactions Bonds Rule Based:

Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.

Hessian Based:

Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.

Angles
Dihedrals

Data

Current Processing StateCompleted
Total Processing Time22:56:04 (hh:mm:ss)

ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Calculated Solvation Free Energy

Access to this feature is currently restricted

Submit New Solvation Free Energy Computation